mesa_cli 0.1.3 → 0.1.4

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -144,6 +144,17 @@ where `INLIST_TO_POINT_TO` is the name of an inlist that you would like your loc
 The `-p` or `--pgstar` option will also point the main `inlist` file to the
 `INLIST_TO_POINT_TO` file for the `pgstar` namelist.
 
+
+### rates
+
+To use, just type
+
+    mesa rates REACTION_NAME OUTFILE
+
+where `REACTION_NAME` is the name of a reaction found in `$MESA_DIR/data/rates_data/cache`, without the preceding `r_` and optionally specifying `_1`, `_2`, or whatever other option is available. For instance, `c12_pg_n13` is a valid `REACTION_NAME`, as is `c12_pg_n13_1`. If no ending number is specified, `_1` is assumed.
+
+`OUTFILE` is an optional argument that specifies a file name where the rate data will be written to. If it is omitted, the data is simply written to the standard output.
+
 ### test
 
 To use, just type

data/bin/mesa

@@ -270,6 +270,95 @@ class MyCLI < Thor
     end
   end
 
+  desc "rates REACTION [OUTFILE]", "Calculate and output out reaction rates"
+
+  long_desc <<-LONGDESC
+  Calls the `show_rates' executable from $MESA_DIR/rates/test for a REACTION
+  found in $MESA_DIR/data/rates_data/cache. The reaction is whatever comes 
+  after "r" or "r_" in the .bin file in the cache directory. You may also
+  include the number at the end if you'd like to specify which rate to use, but 
+  if none is provided, the "_1" option will be used.
+
+  If OUTFILE is provided, the output is redirected to a text file with the name
+  indicated by OUTFILE. Otherwise it is simply written to the screen.
+
+  For example,\n
+  
+  >>> mesa rates c12_pg_n13
+
+  will spit 10,000 lines of rate data to the terminal, while
+
+  >>> mesa rates c12_pg_n13 c12_pg_n13.data
+
+  will save the same data to a file, c12_pg_n13.data.
+  LONGDESC
+
+  def rates(reaction, outfile = '')
+    return unless check_for_mesa_dir
+    cache_dir = File.join(ENV['MESA_DIR'], 'data', 'rates_data', 'cache')
+
+    # set up regular expressions; allow for specific ending number (first case)
+    # or leave it ambiguous (second case)
+    if reaction =~ /_\d$/
+      matcher = /r_?#{reaction}\.bin/
+    else
+      matcher = /r_?#{reaction}_(\d)\.bin/
+    end
+
+    # search for matching cache files. Return if none are found and find lowest
+    # "number" cache file if multiple matches are found
+    rate_files = Dir.entries(cache_dir).select { |f| f =~ matcher }
+    case rate_files.length
+    when 0
+      puts "No reactions matching #{reaction} found in #{cache_dir}. Exiting."
+      return
+    when 1
+      rate_file = File.join(cache_dir, reactions[0])
+    else
+      min_num = nil
+      rate_file = nil
+      rate_files.each do |f|
+        if min_num.nil? or matcher.match(f).captures.first.to_i < min_num
+          min_num = matcher.match(f).captures.first.to_i
+          rate_file = File.join(cache_dir, f)
+        end
+      end
+    end
+
+    data = ''
+    # Execute the `show_rates` function and capture the output
+    visit File.join(ENV['MESA_DIR'], 'rates', 'test') do
+      data = `./show_rates #{rate_file}`
+    end
+
+    # scrub the output for poorly formatted floats
+
+    lines = data.split("\n")[4..-1]
+    t8 = []
+    sigv = []
+    float_matcher = /(\d\.\d+)D?(\-|\+)(\d+)/i
+    lines.each do |line|
+      new_t8, new_sigv = line.split
+      new_t8 =~ float_matcher
+      t8 << $1.to_f * (10**(exp_sign($2) * $3.to_i))
+      new_sigv =~ float_matcher
+      sigv << $1.to_f * (10**(exp_sign($2) * $3.to_i))
+    end
+    lines = t8.zip(sigv).map do |pair|
+      sprintf("%-26.16e", pair[0]) + sprintf("%-26.16e", pair[1])
+    end
+    data = lines.join("\n")
+
+    # save output to screen or to file
+    if outfile.empty?
+      puts data
+    else
+      File.open(outfile, 'w') do |f|
+        f.puts data
+      end
+    end
+  end
+
   private
   def create_ms_file(inlist_name, ms_name)
     ms_name += '.rb' unless ms_name[-3..-1] == '.rb'
@@ -326,7 +415,6 @@ class MyCLI < Thor
 
       # adjust MESA_DIR location and document changes
       lines_to_fix.reverse.each do |i|
-        have_fixed = true
         line = contents[i]
         contents[i].sub!(/=.*/, "=#{dir_name}")
         contents.insert(i, '# ' + "Changed MESA_DIR to #{dir_name} on " +
@@ -363,6 +451,24 @@ class MyCLI < Thor
       "not a supported shell."
     end
   end
+
+  def visit(new_dir)
+    old_dir = Dir.pwd
+    Dir.chdir(new_dir)
+    yield
+    Dir.chdir(old_dir)
+  end
+
+  def exp_sign(str)
+    case str
+    when '-'
+      return -1
+    when '+'
+      return 1
+    else
+      raise "invalid sign: #{exp_sign}"
+    end
+  end
 end
 
 MyCLI.start(ARGV)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: mesa_cli
 version: !ruby/object:Gem::Version
-  version: 0.1.3
+  version: 0.1.4
 platform: ruby
 authors:
 - William Wolf
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-02-10 00:00:00.000000000 Z
+date: 2017-01-31 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: thor
@@ -91,9 +91,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.6
+rubygems_version: 2.6.8
 signing_key: 
 specification_version: 4
 summary: Mesa CLI - a command line interface for simple MESA tasks.
 test_files: []
-has_rdoc: false